fix: writeVcf restores '*' spanning deletion in multi-allele ALT (#65)

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Annotation of Genetic Variants
 Description: Annotate variants, compute amino acid coding changes,
         predict coding outcomes.
-Version: 1.59.0
+Version: 1.59.1
 Authors@R: c(
         person("Valerie", "Oberchain", role="aut"),
         person("Martin", "Morgan", role="aut"),

NEWS

@@ -1,3 +1,18 @@
+CHANGES IN VERSION 1.59.1
+-------------------------
+
+BUG FIXES
+
+    o writeVcf() now restores '*' (spanning deletion) alleles in multi-
+      allele ALT fields instead of writing empty alleles that produce
+      malformed VCF lines (e.g. "CA,,TTA" instead of "CA,*,TTA"). This
+      fixes IGV/htsjdk errors ("empty alleles are not permitted in VCF
+      records") when opening files written by VariantAnnotation.
+      Note: the ambiguous single-allele case (ALT='*' vs ALT='.') cannot
+      be resolved at write time due to read-time representation loss;
+      a future fix at the C parsing level would fully resolve this.
+      (GitHub issue #65)
+
 CHANGES IN VERSION 1.36.0
 -------------------------
 

R/methods-writeVcf.R

@@ -39,6 +39,28 @@
     if (is(ALT, "XStringSetList")) {
         ALT <- as(ALT, "CharacterList")
     }
+    ## Restore '*' for spanning deletion alleles stored as empty strings
+    ## at read time (GitHub issue #65). Per VCF spec, '*' represents a
+    ## spanning deletion allele. At read time, both '*' and '.' (no allele)
+    ## get converted to empty strings, making them indistinguishable.
+    ## Conservative fix: only restore '*' when an empty string appears
+    ## alongside other alleles (multi-allele context), since that's
+    ## unambiguously a spanning deletion. A lone empty string is written
+    ## as '.' to preserve monomorphic reference site semantics.
+    if (is(ALT, "CharacterList") || is(ALT, "List")) {
+        ALT <- endoapply(ALT, function(a) {
+            empty <- !is.na(a) & nchar(a) == 0L
+            if (any(empty) && length(a) > 1L)
+                a[empty] <- "*"
+            a
+        })
+    } else if (is.character(ALT)) {
+        ## ExpandedVCF: scalar character per row — ambiguous case.
+        ## These are already expanded so a single '*' would have been
+        ## the only allele for that row. Write as '*' since expand()
+        ## doesn't produce monomorphic rows.
+        ALT[!is.na(ALT) & nchar(ALT) == 0L] <- "*"
+    }
     ALT <- as.character(unstrsplit(ALT, ","))
     ALT[nchar(ALT) == 0L | is.na(ALT)] <- "."
     if (is.null(QUAL <- qual(obj)))